open my $f1, '<', \<<'';
string1 (C)C(T)A
string2 T(A)GG(A)GGG(G)

open my $f2, '<', \<<'';
string1 1 C A
string1 3 T C
string2 5 A T
string2 9 G A
string2 2 A C

my %h = map split, <$f1>;
tr/()//d, $_ = [split //] for values %h;

while (<$f2>) {
    local $" = ',';
    my ($k, $i, @combo) = split;
    $h{$k}[$i-1] = lc "{@combo}";
}

for my $k (sort keys %h) {
    local $" = '';
    while (<@{$h{$k}}>) {
        s/([a-z])/(\u$1)/g;
        print "$k $_\n";
    }
}